The dynamics of microfilament (<5 mm) ingestion were evaluated in three species of snooks. The ingestion of different colours and sizes of microfilaments were strongly associated with the spatio-temporal estuarine use and ontogenetic shifts of snooks. Their feeding ecology was also analysed to assess dietary relationships with patterns of contamination. All species were highly contaminated with microfilaments. The highest ingestion of microfilaments occurred in the adults, when fishes became the main prey item and also during the peak of fishing activities, in the rainy season. This suggests that trophic transfer, in addition to periods of high availability of microfilaments are important pathways for contamination. The ingestion of microfilaments of different colours and sizes was likely influenced by input sources. Blue microfilaments were frequently ingested, and appear to have both riverine and estuarine inputs, since they were ingested in all seasons and habitats. Purple and red microfilaments were more frequently ingested in the lower estuarine habitats. The length of microfilaments was also associated with environmental variability. Longer microfilaments were ingested in habitats with greater riverine influence, the opposite was observed for shorter microfilaments. Therefore, microfilament contamination in snooks are a consequence of their ecological patterns of estuarine uses through different seasons and life history stages.