Freshwater mussels (Unionida) can strongly affect nutrient cycling in temperate ecosystems but data from the tropics is lacking. We quantified the effects of mussel filtration, excretion and biodeposition on nutrient and photosynthetic pigment concentrations in a tropical eutrophic lake and mesotrophic river, featuring one non-native and two native species, respectively. Changes in nutrient and pigment concentrations were measured over a 3 h period to assess effects on (1) the water column in field enclosures, and (2) water column and benthos combined in controlled laboratory experiments. In field enclosures in both systems, mussel density and biomass were significantly correlated with the magnitude of reduction in sestonic pigment concentrations. In laboratory experiments, presence of mussels led to reduced PO4 and increased TAN concentrations in both systems, lower combined sestonic and deposited pigment concentrations in the river but increases in the same in the lake. We conclude that excretion by mussels probably accelerated bioseston growth in both systems due to N-fertilisation, an effect that may be particularly common in tropical freshwaters, which are frequently N-limited. However, whilst river mussels reduced bioseston concentrations through rapid filtration, higher rates of N-excretion and/or deposition of undigested bioseston by lake mussels apparently resulted in a net increase of pigment concentrations.