As vectors for microorganisms and genetic elements, vast amounts of solid wastes, including plastics and non-plastics, enter oceans through estuaries globally. The heterogeneity of microbiomes developed on different types of plastic and non-plastic matrices and their potential environmental risks in field estuarine regions have not been fully explored. Here, microbial communities, antibiotic resistance genes (ARGs), virulence factors (VFs), and mobile genetic elements (MGEs) on substrate debris (SD) covering non-biodegradable plastics, biodegradable plastics, and non-plastics were first comprehensively characterized based on metagenomic analyzes (substrate identity). These selected substrates were field-exposed at both ends of the Haihe Estuary, China (geographic location). For substrate identity: conspicuously diverse functional gene profiles on different substrates were obtained; the relative gene copies of ARGs, VFs, and MGEs on non-biodegradable plastics were highest at both locations; non-biodegradable plastic matrices recruited the most abundant unique ARGs from ambient waters; the relative abundance of potential bacterial hosts carrying multiple ARGs and VFs (BH-AV) was much higher on non-biodegradable plastic surfaces than on the other two substrates, especially in the coastal water environment. For geographic locations: more abundant specific ARGs, VFs, and MGEs were significantly enriched on SD from the upper estuary; the average relative abundance of identified BH-AV on SD from the upper estuary was 1.99-7.14 folds from the lower estuary. Finally, the results of the Projection Pursuit Regression model verified the higher comprehensive potential risks arising from non-biodegradable plastics (substrate identity) and SD from the upstream of the estuary (geographic location). Based on comparative analysis, our results alert us to pay particular attention to ecological risks triggered by conventional non-biodegradable plastics in rivers and coastal environments and highlight the microbiological risk from terrestrial solid waste to the downstream marine environment.