Understanding environmental drivers of fish assemblage composition is fundamental to designing useful management plans for anthropogenic activities. This study investigated the influence of suspended sediment on reef fish assemblages and habitat composition over a cross-shelf turbidity gradient in the nearshore Pilbara region of Western Australia. The responses of all feeding guilds were analysed to identify feeding guilds vulnerable to elevations in suspended sediment and sedimentation. This study is the first of its kind to utilise both remotely sensed and in situ turbidity data to characterise the general turbidity regime and magnitude of stochastic events. By using the coordinates from a principle coordinates analysis, we were able to capture both the general turbidity conditions and stochastic turbidity spikes at each site, whilst the use of in situ turbidity measurements allowed us to effectively ‘ground-truth’ the remotely sensed TSS data. Underwater visual census was used to sample the fish assemblage and quantify habitat across the turbidity gradient. Generalised additive mixed models were used to explore the relationships between environmental variables, habitat variables, and fish assemblage metrics. Species richness significantly declined with increasing levels of turbidity. This study identified two key functional groups of fish that are vulnerable to elevated suspended sediment loads. Planktivorous omnivores and herbivorous scrapers decreased in abundance at high turbidity sites. Total biomass of herbivorous scrapers was lower at turbid sites, whilst the biomass of planktivorous omnivores was not related to any of the predictor variables. Changes in the abundance, biomass, and behaviour of these functional groups can have severe consequences for the resilience and recovery of coral reefs. Anthropogenic activities that elevate suspended sediment in regions where coral reef communities exist should consider these implications when designing management plans.