5 Start-up Guide

- Basic Operation
- Filtration
- Sump Flow
- Mesocosm Tank Flow
- CO2 Scrubber to Elevate pH
- Draining the Meso and Sump

Basic Operation

  1. Operating water level in the filtration sump should be at least 7" in the filter cell compartment, about 2 inches above the three carbon filters.
  2. Outflow water from the tanks feeds down to the outside underground sump pump, then into to the filtration system inside the Citrus Hall Field Room.
  3. Water pumped into the Field Room flows through three 50um bag filters and eight matala mesh filters before overflowing into the main holding reservoir. Reservoir water is pumped through three carbon filters, a UV sterilizer, and chiller, then either back into the holding reservoir or to the tanks.
  4. Water directed toward the tanks has two potential inflow ports (one constant flow and one controlled by a solenoid) and two potential outflow ports (one overflow port and one controlled by a manual open/close needle valve to adjust tank volume)


  • Biological and Mechanical Filtration: Water from the Mesocosm tanks is pumped into the sump while passing through three 50um bag filters and eight matala mesh filters (high and low density) to pick up debris. These filters have an accumulated biofilm to biologically filter the water before entering the sump and returning to the tanks.
  • Chemical and Mechanical Filtration: Water in the sump is pulled through three carbon filters with mesh filter sleeves and pumped into a UV sterilizer before entering the sump and returning to the tanks.

Sump Flow

  1. Preparing flow in the sump
    1. Before turning on the pump, make sure the correct channels of flow are opened to direct the water where it needs to go.
    2. The Meso Return valve should be vertical in the “closed” position (perpendicular to the PVC), and the Sump Return valve should also be vertical in the “open” position (in line with the PVC). See Figure 1 to identify valves.
    3. The Pump Return valve should be veritcal in the “open” position to allow flow from the sump through the pump to the UV filter and chiller compartments. See Figure 2.
      1. If you do not intend to utilize the Secondary Sump at this time, close the Sump Exchange valve (as shown in Figure 2)
    4. The two UV Flow valves and the Chiller Bypass valve should all be vertical. This directs flow down through the UV light chamber before pushing through to the chiller compartment. See Figure 3.
      Figure 1. Sump Flow Valves
      Figure 2. Pump Return Valve
      Figure 3. UV Flow and Chiller Bypass Valves
  2. Turning on sump flow
    1. Once all the valves are properly opened/closed as described above, plug in the Cascade Pump and make sure water is running through the system properly without any leaks. There may be some initial sputtering while air is pumped out of the pipes, but that should stop within a couple minutes.
    2. Look at the pump and make sure you can see water being pushed through the clear junction.
      1. If it looks like water is not running through the pump, unplug the pump immediately. Running the pump dry can burn out the motor.
    3. If everything seems to be stable, plug in the UV light.
    4. To stabilize the pH in the system, fill the PhosBan Reactors with CO2 absorption media and plug in the air pumps as detailed below.

Mesocosm Tank Flow

  1. Filling the mesocosm tanks
    1. Make sure the drain valve located under each tank is closed (turned clockwise all the way, finger-tight).
    2. Fill each rack one at a time (only open the N flow valves for one set of 4 tanks at a time) and make sure rack and filtration skid flows are balanced before moving on to the next rack.
      1. Open the N flow valve for each tank (and S flow valve if you plan to turn on the solenoid [SOL-TNK-#] to help fill the tanks).
    3. To open flow from the sump to the tanks, first make sure the circular flow within the sump itself is stable. Then slowly open the Meso Return valve (turn counterclockwise) until the t-valve is sitting about 45 degrees to the PVC pipe. This configuration splits flow to both the sump and the mesocosm. You can further adjust water pressure to the tanks by slightly closing the Sump Return valve to direct more flow to the meso, less flow to the sump, while always keeping the line to the sump partially open.
    4. Once all tanks are filled, make sure the whole system is stable in standard recirculation mode before setting up a tidal cycle, if desired.
  2. Set flow in tanks
    1. Calculate your desired residence time. When full, each tank holds 55 liters, so divide 55L by your desired residence time and use that estimated value as your flow rate. Example: for a RT of 4 hours: 55L/4hr = 13.75 L/hr
    2. Use the Neptune Systems flow meters as a guide for setting the flow, but for the most accurate flow rates, use a graduated cylinder to estimate flow into each tank.
      1. Using the example above: 13.75 L/hr = 229.2 mL/min = 38.2 mL/10 seconds to efficiently check each tank’s flow using a graduated cylinder
    3. While higher flow is more stable, lower flow may change slightly throughout the day, so it is recommended to check and set flow twice per day: once in the morning and once in the afternoon/evening.

CO2 Scrubber to Elevate pH

  1. Filling/Replacing media in the Phosban Reactor
    1. Unplug the airpump connected to the Phosban Reactor and disconnect both sets of tubing going into/out of the Reactor to easily handle it.
    2. Unscrew the lid of the Reactor, take off the red cap and black mesh, and pour out the used up media (purple if freshly used, grayish white if used and stale) into a bag or some other containment. Used media can be deposited in a standard trash receptacle.
    3. Use tape or parafilm to cover the hole of the small tube inside the Reactor before pouring in the new media (stark white pellets). Fill to an inch below the top of the small tube, so no media falls into the tube. Remove the covering from the small tube and replace the black mesh and red cap, aligning the red cap so it encapsulates the top of the small tube.
    4. Screw the lid back on, finger tight, and replace the Reactor on the side of the sump. Reconnect the tubing from the airpump to the side of the Reactor and from the air splitter to the front of the Reactor. Submerge the airstones connected to the air splitter tubing in the holding reservoir of the sump.
    5. Once you’re sure everything’s securely placed, plug in the air pump.
    6. Listen and feel for any air leaks and adjust tubing as necessary.

Draining the Mesocosm and Sump

  1. The first step before draining any water is to turn off the powerheads, heaters, and CO2 solenoids in all mesocosm tanks. The powerheads and heaters cannot be ON when dry or they may be damaged.
  2. You must also place caps on each pH probe filled with either DI water for temporary storage or KCl storage solution for long-term storage. The probe tips cannot dry out or they will be damaged.
  3. When draining the tanks, drain one rack of 4 tanks at a time, to not overflow the drainage system.
    1. If you intend to only drain the mesocosm tanks, but not the sump, then first make sure the Sump Return valve of the filtration system is fully open (parallel to the PVC), then turn off the flow of both the N and S valves for each tank, turning the valves clockwise, and remove the outflow pipes as described below. If needed, divert excess water into the secondary sump following the “Overflow” steps below, and disregard the rest of these draining instructions.
    2. If you intend to drain the sump as well to fully shut down or clean out the system, then maintain high flow through the N valve into all tanks. Continue following this set of instructions.
  4. Divert flow from the mesocosm tanks to the drainage port
    1. There is a drain in the Mechanical Room behind the Field Room with PVC pipe facing downward inside. This PVC is connected to our system and is the location for all system drainage.
    2. Refer to Figure 1. for the following t-valve identities.
    3. First open the System Drain Valve by turning the valve so it aligns parallel to the PVC. This opens flow to the drainage port in the back room. Always open an avenue of flow before closing an avenue of flow to avoid back pressure build up.
    4. Second, partially close the Meso To Sump valve by turning the valve so it sits diagonal to the PVC. This will reduce incoming water from the mesocosm from entering the sump and will divert some flow out of the system.
      1. Do not yet close the Meso To Sump valve completely until you can ensure there is no overflow at the drainage port in the Mechanical Room.
  5. Open tank drains
    1. Under each tank is a needle valve controlling drain flow through the smaller outflow pipe in each tank. Fully open this valve for the rack of 4 tanks, turning the needle counterclockwise.
  6. Removing the outflow pipes
    1. In each of the four tanks, unscrew the larger outflow pipe until it is fully removed and water in the tank can drain out from the lowest point in the tank.
    2. The smaller outflow tube can simply be pulled out from its slot, sometimes needing to be twisted to be unwedged.
  7. The sump pump located in the ground between the Mesocosm container and the Field Room will funcition normally to push water from the tanks to the Field Room system, but as you drain large volumes of water, periodically check that the water is not overflowing out of this in-ground reservoir.
  8. Also periodically check the drainage port to make sure the water pumped from the tanks is not overflowing onto the floor of the Mechanical Room.
    1. If you notice water is overflowing, slightly open the Meso To Sump valve to divert some water back into the sump and reduce the water volume diverted to the drainage port.
    2. Do not allow salt water to overflow the drainage port of the Mechanics room
  9. Unplug the UV light and air pumps, but leave the water pump on for now.
    1. Allow the sump to continue pumping water from the main reservoir into the tanks, where the water will continuously drain out of the system.
  10. Once the water level in the sump is about an inch or two below the top of the carbon filters (the three white cylinders inside the sump), unplug the Pump. The pump must be turned off before it runs dry, otherwise the pump will be damanged
    1. At this point there will still be some water left in the sump, which can either be siphoned out and dumped into the drainage port, or you can use a small aquarium pump to pull water out of the main reservoir and the mesh filtration reservoirs.
    2. Be cautious to not let this pump run dry either, or it may be damaged
    3. To access the bio-filtration reservoir, remove the black and blue matala mesh filters, and clean them by hosing them down with freshwater (available just outside the Field Room door).
    4. To access the 50-micron mesh reservoir, remove the PVC pipe located directly after the Meso To Sump valve (see Figure 1) by unscrewing the PVC at the junction. This PVC pipe with three outports can be temporarily removed, so the mesh can be taken out and also sprayed down to clean.
    5. Remove the three carbon filters from the main reservoir to hose them down to clean.
  11. Post-drainage
    1. Once the system is fully drained of seawater, screw back on the PVC pipe with three outports at the junction by the Meso To Sump valve. Also re-place each mesocosm tank’s outflow pipes (screw in the large pipes and wedge in the small pipes).
    2. Follow the instructions in the Water Collection Guide for filling the sump with fresh water (attach a hose to the water pipe next to the Field Room door and fill the sump from the hose) and the order of operations for turning flow back on through the sump and tanks.
    3. You will not have to plug in the UV light or air pumps since you are not maintaining any water chemistry, but rather just flushing the system.
    4. Let fresh water run through the system for one to two days before following these same steps for draining the freshwater.
  12. Once the system has been flushed with fresh water and drained again, remove the water inflow tubes from each tank’s N and S ports to be acid washed and rinsed in DI water before next use.

Overflow into Secondary Sump

  1. If you need to contain more water in the system than the tanks and main reservoir can hold at one time (ex. during a “low tide event” when half of the tank water is drained into the sump), then you will need to incorporate flow to and from the secondary sump.
  2. First unplug the sump’s main water pump to make sure the pump will not run dry if the water level drops too low (see details below).
  3. To direct some flow from the mesocosm system into the secondary sump, partially or fully open the Secondary Sump Return valve (Figure 1), so that the t-valve runs parallel with the PVC. Filtered sump water will then be simultaniously directed into the mesocosm and the secondary sump, via PVC tubing that diverts water into the top of the secondary reservoir.
  4. To then open flow between both the main holding reservoir and the secondary sump, open the Sump Exchange valve (Figure 2), so the t-valve runs parallel with the PVC.
    1. Because this flow-through connection will allow water to flow between both reservoirs to establish water level equilibrium, make sure the water level in the main reservoir is still about 2 inches above the carbon filters after this water exchange has occurred. If not, add more seawater to the system until the carbon filters are once again submerged to avoid the pump running dry.
    2. Once the carbon filters are appropriately submerged (seawater just two inches above the filters, not much more), turn the main pump back on.
    3. The full system requires ~ 400 gallons of sea water to maintain tank volume and submersion of carbon filters while including use of the secondary sump.