Estuaries and salt marshes are important coastal ecosystems that present unique characteristics in terms of nutrient cycling, salinity, habitats, flora and fauna. Despite their ecological importance, there is scarce knowledge on the occupation, distribution and ecology of insects, including Tipuloidea, in these environments. This study aimed to evaluate the composition, seasonality and effect of abiotic factors on the abundance, diversity and structure of a Tipuloidea assemblage at the Patos Lagoon salt marshes, located at the south of the Neotropical region. We sampled crane-flies from three zones along the estuary by installing two Malaise traps at the low and high vegetation strata of each zone. Sampling was conducted uninterruptedly every fifteen days between August/2015 and July/2016, and collected insects were identified morphologically based on specific literature. 5248 crane-flies were identified covering six species and twenty-five morphospecies. Abundance and frenquency of occurrence of species revealed a gap in the presence of constant species at the middle estuary. Dicranomyia, Gonomyia, Teucholabis and Zelandotipula species were additional (accessory) species only in the upper estuary, while Symplecta cana only in the lower estuary. This shows that different species prefer distinct points along the estuary. Higher abundance of crane-flies was correlated with elevated temperature and humidity. Symplecta pilipes was an exception, presenting increase in abundance under lower temperatures. Seasonal change in Tipuloidea species composition was observed, with higher evenness of Dicranomyia, Geranomyia, Rhipidia domestica and Symplecta cana (15–20%) during summer, and dominance of Symplecta pilipes in winter (80%). The gap at the middle estuary can possibly be due to stress caused by large fluctuations in salinity in the zone. In addition, the seasonal differences can have significant ecological consequences such as the modification of the Tipuloid species that compose the detritivorous and/or succivorous trophic guild, and consequently influence the upper trophic levels of the salt marsh environment.