In order to investigate spatiotemporal co-occurrence patterns of demersal fishes from the Paranaguá Estuarine Complex (PEC) and the adjacent continental shelf, state of Paraná, Southern Brazil, fish from nine sampling sites within the estuary and three additional sites in open sea (N = 12 sampling sites) were sampled at quarterly intervals between 2014 and 2016. The assemblage structure was evaluated by the C-Score index and null models developed through 5,000 randomizations. Species co-occurred as expected, but a general pattern in both temporal and spatial matrices was only detected in the Upper sector, which showed a random co-occurrence pattern. In contrast, fish species from the other sectors co-occurred less than expected by chance in some circumstances. According to the concepts related to the organization of communities on temporal scales, many communities tend to become disorganized after disturbances and then present a progressive increase in organization, that is, they display a random co-occurrence pattern, similar to initial response, and over time the species in the community segregate or aggregate in response to system stability restoration. Therefore, understanding how fish assemblages are structured at different spatial and temporal scales, and especially what processes drive such conformations, including assembly rules for communities, is crucial for ecosystem maintenance and understanding, as well as providing baselines for conservation and management policies, interventions, and practices in these environments.