Long-term fish assemblage monitoring requires investigators account for within-year variation in species' detection. An occupancy modelling framework is presented that accounts for variation in species presence and estimates the effort required to minimise within-year variation. Species detections from snorkelling surveys and an electrofishing survey were used in single-species occupancy models to determine the importance of site and sampling covariates on species' occupancy (psi) and detection probabilities (p). Community occupancy models estimated species richness in light of undetected species. For most species, models including patch size and reach as psi-covariates had higher support whereas models including patch size and sampling method as p-covariates had higher support. The number of sites and repeated surveys required to estimate occupancy accurately varied among fish species. Community models suggested that the observed number of species underestimated actual richness as much as 27% and the addition of an electrofishing survey increased estimated richness by 13%.