Microplastic contamination in the intertidal zone of beaches and estuaries has been reported worldwide. Nonetheless, evidence of patterns in the small-scale distribution of microplastics within the intertidal zone is often contradictory. When such conflicting evidence is used to inform sampling campaigns, it increases uncertainty in resulting data. Moreover, the conflicting patterns hamper efforts in spatially explicit risk characterization of microplastic pollution to intertidal organisms. This study aimed to analyze spatial patterns in microplastic concentrations within the intertidal of beaches and estuaries. A laboratory protocol for cost-effective identification and quantification of microplastics from sediments was developed and validated. This protocol was used to sample microplastic concentrations in sediments at intermediate (60 m transects) and local (1 m2 quadrats) scales across sites with varying levels of urbanization. Large (5.0 mm – 0.5 mm) and small (0.5 mm – 0.125 mm) microplastics were quantified using the protocol, and smaller microplastics (≥ 0.033 mm) could be detected. Polymers with densities higher and lower than seawater were encountered in roughly equal proportions in both ecosystems. Our results suggest that sufficient sample replication is needed to account for the high variability in microplastic concentrations at local scale. Moreover, despite the drift zone often being targeted during microplastic monitoring, microplastic concentrations varied across beach zones without evidence of accumulation at the drift zone. Alternatively, local environmental factors such as sediment grain size and structural complexity of estuarine habitats, and the presence of larger plastics as a local source of microplastics, related to measured concentrations in microplastics. We recommend that samples should be spread across the intertidal to account for small scale variability, and that local environmental variables should be considered as confounding factors when comparing contamination levels among beaches or estuaries.