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Terrestrial runoff into aquatic ecosystems may have both stimulatory and inhibitory effects, due to nutrient subsidies and increased light attenuation. To disentangle the effects of runoff on microbenthos, we added soil to coastal mesocosms and manipulated substrate depth. To test if fish interacted with runoff effects, we manipulated fish presence. Soil decreased microphytobenthic chlorophyll-a per area and per carbon (C) unit, increased microbenthic phosphorous (P), and reduced microbenthic nitrogen (N) content. Depth had a strong effect on the microbenthos, with shallow substrates exhibiting greater microbenthic net ecosystem production, gross primary production, and community respiration than deep substrates. Over time, micobenthic algae compensated for deeper substrate depth through increased chlorophyll-a synthesis, but despite algal shade compensation, the soil treatment still appeared to reduce the depth where microbenthos switched from net autotrophy to net heterotrophy. Fish interacted with soil in affecting microbenthic nutrient composition. Fish presence reduced microbenthic C/P ratios only in the no soil treatment, probably since soil nutrients masked the positive effects of fish excreta on microbenthos. Soil reduced microbenthic N/P ratios only in the absence of fish. Our study demonstrates the importance of light for the composition and productivity of microbenthos but finds little evidence for positive runoff subsidy effects.