December 11, 2013

When the Fish and Plants Don’t Get Along

Laura Genello

Laura Genello

Guest Blogger

Johns Hopkins Center for a Livable Future

2013-aquaponics-tankIt’s easy to get excited about aquaponics. On the surface it seems simple: the waste from the fish is recycled into valuable nutrients for the plants, while the vegetables purify the water for the fish. Aquaponics, like any form of agriculture, is dynamic, changing with the seasons and over time. As the fish and plants grow, their needs change and shift the balance.

There are three primary living components of an aquaponics system: the fish, the bacteria that break down the fish waste, and the plants. These three components depend on one another, yet also have diverse and sometimes conflicting needs. Our tilapia need clean water free of the toxins that they excrete (like ammonia), plenty of dissolved oxygen, a steady neutral pH, just the right amount of food, and a consistently warm water temperature.  The water from the fish tanks passes through a filter system where bacteria convert the ammonia from the fish waste into a non-toxic form of nitrogen that the plants use. These bacteria have many of the same needs as the fish, but they also require a steady supply of ammonia on which to feed. The plants in turn require a steady supply of nutrients, including nitrate, the waste product of the bacteria.

Small changes can upset the balance.  A sudden drop in temperature might kill members of the bacterial community. Harvesting too many fish at once can send the nutrient levels plummeting because fewer fish produce less waste, which starves both bacteria and plants of nutrient. A pest outbreak that unexpectedly kills a crop is detrimental to water quality.

Backup systems, robust system design, and good management practices are all important for maintaining dynamic balance, but even so, it is not always easy. We constantly monitor our water quality, fish health, and plant performance to ensure that we are keeping the system balanced, but what happens when something goes wrong?

Earlier this fall, we found that our ammonia levels were rising, hovering between 0.15 – 0.25 ppm (or 0.15 – 0.25 mg/L). While these levels are too low to be toxic to tilapia, the increasing levels were indicative that something was wrong. We decreased our feeding rate, but the ammonia levels still remained high, and our fish and plants weren’t receiving the nutrient inputs that they need. However, in the same period of time we had accumulated a fair amount of fine solids from fish waste and decomposing plant material on the bottom of our plant beds. This sludge will form an anaerobic (oxygen free) zone, attracting bacteria that will actually release ammonia back into the water as they break down the solids. Earlier this week, we cleaned out 12 gallons of sludge from our plant beds, and our ammonia levels dropped dramatically overnight, from 0.28 ppm to 0.04 ppm, bringing them back down to a level where we are comfortable.

It is likely that the solid sludge on the bottom of our plant beds was the most important factor, in this case, but it was not the only factor at play. Water quality dynamics and the balance between the diverse living things that make up an aquaponics system are complicated. The complex natural systems that we are emulating are exponentially more complicated than even our 4,000-gallon experiment in ecological agriculture. Now in our second season, we are still learning what works and what doesn’t. Like any type of farming, it can take years to master the idiosyncrasies at play with your particular land, climate, and growing conditions.


  1. Posted by Juan Saavedra

    Hello how are you? Wow, Aquaculture in Baltimore, that is awesome. I would love to go and see what you are doing. Would I be able to visit say, tomorrow?

  2. Laura Genello

    Posted by Laura Genello

    Hi Juan, we love having visitors at the aquaponics project, but today is not a good day to visit. The best time to come would be during our weekly Wednesday Open Hours, from 10am – noon. Because of the holidays, we will not be holding open hours on Wednesday 12/25 or 1/1. Our next open hours will be held on January 8th. If that does not work for you, please email me at and we can set up another time for you to come out.

  3. Thank you for saying this! Sediment is very common in AP systems but it’s very damaging for several reasons. (Just for fun let’s talk about more of them. : )

    Pathogens that attack plant roots (Pythium and Phytophthora), as well as human GI pathogens (Salmonella, E. coli, Listeria, etc) have a much easier time living in sediment than in clean systems.

    As well as releasing ammonia, the sediment also consumes oxygen as it decays. Roots in hydroponics with low oxygen are very vulnerable to the same exact pathogens that live in sediment– Pythium and Phytophthora. These diseases are devastating and once the conditions are right they strike FAST. One day the plants are good, the next their roots are all brown slime and the plants are wilting on top of a bed of water.

    Letting sediment build up in your system is an invitation to major disaster. And diarrhea and vomiting. To be avoided.

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