The ecological risks of biodegradable microplastics (BMPs) to soil ecosystems have received increasing attention. This study investigates the impacts of polylactic acid microplastics (PLA-MPs) and polybutylene adipate terephthalate microplastics (PBAT-MPs) on soil properties of black soil (BS) and fluvo-aquic soil (FS) under three water conditions including dry (Dry), flooded (FL), and alternate wetting and drying (AWD). The results show that BMPs exhibited more evident aging under Dry and AWD conditions compared to FL condition. However, BMPs aging under FL condition induced more substantial changes in soil properties, especially dissolved organic carbon (DOC) concentrations, than under Dry and AWD conditions. BMPs also increased the humification degree of soil dissolved organic matter (DOM), particularly in BS. Metagenomic analysis of PBAT-MPs treatments showed different changes in microbial community structure depending on soil moisture. Under Dry conditions, PBAT-MPs enhance the ammonium-producing process of soil microbial communities. Genes related to N nitrification and benzene degradation were enriched under AWD conditions. In contrast, PBAT-MPs do not change the abundance of genes related to the N cycle under FL conditions but significantly reduce genes related to benzene degradation. This reduction in benzene degradation genes under FL condition might potentially slow down the degradation of PBAT-MPs, and could lead to temporary accumulation of benzene-related intermediates. These findings highlight the complex interactions between BMPs, soil properties, and microbial communities, emphasizing the need for comprehensive evaluations of BMPs' environmental impacts under varying soil water conditions.