3D Pond Ecosystem: Food Web, Daphnia, Fish, Algal Bloom and Oxygen Lab

Setting up the lab bench...

Presets

Live readouts

Graphs

Nutrient, algae, zooplankton, fish and detritus

Dissolved oxygen: surface, bottom, saturation

Algae-zooplankton phase plane

Light profile with depth of the water body

Chlorophyll-a and Secchi depth (trophic state)

Numerical checks

running...

How to use

Pick a preset and watch the cross-section: algae (green dots) make the water green, the Secchi disk shows how deep you can see, zooplankton and fish appear in proportion to their biomass, detritus builds up on the bottom and fish gasp at the surface if the bottom water runs out of oxygen. The food-web diagram under the pond shows the fluxes between compartments in mg/L per day. You can change nutrients, flushing, depth, turbidity, mixing, climate and the organisms' rates while it runs; the buttons add a nutrient pulse, stock fish or remove them. Drag to orbit, wheel to zoom. Space pauses, R restarts. Things to try: (1) Healthy pond, then raise nutrient loading step by step and watch chlorophyll and Secchi depth; (2) Remove the fish and see the water clear after a few weeks; (3) Stratified summer for hypoxia, then raise the mixing slider; (4) switch on the seasons for a spring bloom; (5) raise flushing until the algae wash out; (6) press the nutrient pulse and follow the bloom and crash.

The pond basin with its sediment and stones, the roach-like fish, the water flea Daphnia (shell, antennae, eye and brood chamber), reeds with their seed heads, lily pads and the algal cell clusters were modelled in Blender 5.2 with baked PBR textures and exported as one Draco GLB. Three.js r160 instances the organisms from the same ecosystem model as the 2D page, tints the water by chlorophyll and detritus, shows the Secchi disk and lets you cut through the water column.

The science

A pond or lake is a small food web driven by sunlight and nutrients. This model follows six quantities in the mixed layer in mg of carbon-equivalent per litre: dissolved nutrient N (carbon-equivalent through the Redfield ratio), algae P (phytoplankton), zooplankton Z (Daphnia and relatives), planktivorous fish F, detritus D, and dissolved oxygen in the surface water and in the bottom water.

Algal growth is the product of a nutrient term and a light term, scaled by temperature:

growth = μ_max f(T) [N/(k_N + N)] [I/(k_I + I)] P, f(T) = 1.0663^{(T − 20)}

The light is the depth-average of the Beer-Lambert profile over a mixed layer of depth H, with attenuation k = k_w + k_cP (water plus self-shading by the algae):

I = I₀ (1 − e^−kH) / (kH)

so more algae make the water murkier and eventually limit their own growth; the lowest of the nutrient and light factors tells you what limits the bloom (shown in the readout). Grazing and predation use Holling type II (saturating) responses: zooplankton eat algae at g_maxf(T) P/(k_P + P) Z, a fraction α becoming zooplankton biomass and the rest being excreted or egested; fish eat zooplankton the same way with their own efficiency. Mortality closes the cycle: dead material becomes detritus, which settles (and is regenerated in the sediment) and is remineralised at a temperature-dependent rate back into nutrient. With no inflow or outflow the sum N + P + Z + F + D is exactly conserved (check 1).

Oxygen. Algae release oxygen in proportion to their growth (2.67 g O₂ per g C); respiration, decomposition and grazing consume it; exchange with the air restores it toward saturation, O_sat(T) = 14.62 − 0.3898T + 0.006969T² − 0.00005897T³ mg/L (about 9.1 at 20 C, lower when warm). The bottom water has a second reservoir that is fed oxygen only through vertical mixing and loses it to the decay of settling detritus; when the water is warm, productive and stratified (low mixing) it drops below 2 mg/L (hypoxia), the cause of fish kills in eutrophic lakes.

What it shows. More nutrient loading gives more algae and murkier water (eutrophication; chlorophyll-a and Secchi depth classify the trophic state). The trophic cascade: fish eat zooplankton, so removing the fish lets zooplankton graze the algae down and the water clears (biomanipulation), while too many fish make blooms worse. With the seasonal cycle on, light and temperature follow a sine over the year and a spring bloom appears. Flushing washes organisms out at the dilution rate D: a population can only persist if its growth exceeds D.

Numerical checks run in the page. (1) mass conservation in a closed pond over 60 days; (2) oxygen reaeration against the exponential solution; (3) the chemostat equilibrium N* = k_N(D + m)/(μ − D − m) of the algae-only system; (4) Smith's average light against numerical integration of the Beer-Lambert profile; (5) the 1.0663 temperature law and the saturation value at 20 C; (6) more nutrient loading gives more plankton at equilibrium; (7) the trophic cascade (removing fish lowers algae).

Simplifications. A single well-mixed layer (plus one bottom reservoir) with no explicit depth profile or day-night cycle; all biomass in carbon units with fixed stoichiometry; one algal, one grazer and one fish group (no cyanobacteria, macrophytes or benthos); fish are a lumped biomass with no age structure, no migration and no mortality from hypoxia in the biomass equations (the picture shows it); parameter values are plausible round numbers in the range of textbook models (Franks-type NPZ), not fitted to a lake. The animated plankton and fish are illustrations drawn from the biomasses.