Although in situ sediment capping is frequently used to reduce internal loading of contaminants and nutrients, post-application assessment rarely includes the potential undesirable short-term effects on plankton species composition. We hypothesised that a modified zeolite (Z2G1) application as a sediment capping agent in Lake Okaro, New Zealand, could cause significant undesirable shifts in species composition of both zooplankton and phytoplankton due to burial of resting stages or interference with feeding for the zooplankton. Alternatively, we predicted that the capping agent might have no effect due to, for example, the coarse grain size of the material (1–3 mm). We used multidimensional scaling (MDS) and analysis of similarity (ANOSIM) to identify any adverse effects of Z2G1 on zooplankton and phytoplankton species composition (i.e. shifts in community structure, including species loss) by comparing the community structure before and after the Z2G1 application. We found no significant differences in species composition before and after the Z2G1 application at the depths investigated (surface and 9 m). However, all of the analyses showed statistically significant differences among seasons, indicating seasonal variations in plankton composition far outweigh those that may have resulted from the Z2G1 application. Coarse particle size, low dose rate and a restricted area where the sediment capping agent was applied were considered to be the factors limiting potential adverse effects on plankton species. Considerations of finer-grained material to increase coverage and efficacy of phosphorus adsorption require assessment for their effects on zooplankton, however, and a direct mode of application into the hypolimnion is recommended to minimise effects on zooplankton and phytoplankton communities.