Environmental factors and microorganisms play a pivotal role in shaping soil microbial diversity. Variables like temperature, moisture, pH levels, organic matter, and the presence of organisms influence the types and abundance of microbial life in the soil. This research was aimed at assessing the impact of soil depth and environmental factors on microbial diversity and physiochemical properties of agricultural soils. A total of 27 samples were collected at various depths of (0-15, 15-30 and 30-60cm), the samples were subjected to standard laboratory analysis using standard procedures. The temperature of tomatoes field soils ranged from 14-31oC, rice field soils 15-36oC and corn field soils 12-24oC. The pH of tomatoes field soils varied from 4.8-8.0, rice field soils 3.8-6.8 while corn field soils were 5.8-8.1. The moisture content of the tomatoes field soils ranged from 20-33%, rice field soils 17-28%, and corn field soils 10-22%. Organic carbon of tomatoes field soil varied from 6.35-6-61, rice field soil 6.20-6.60 and corn field soils 5.88-6.96, Organic matter for tomatoes field soils varied from 10.93-11.39%, rice field soils 10.74-11.38% while corn field soils 10.14-11.53%. Nitrogen of tomatoes field soils ranged from 0.46-0.43mg/kg, rice field soils 0.42-0.43mg/kg and corn field soils 0.38-0.56mg/kg. The phosphorus content of the tomatoes field soil ranged from 0.06-0.07mg/kg, rice field soils 0.06-0.06mg/kg while corn field soils 0.06-0.07mg/kg. The tomatoes field soil total fungal count based on various depths varied from 2×106(cfu/mL) - 1×106(cfu/mL), the rice field varied from 2×106(cfu/mL) - 1×106(cfu/mL) while the corn field varied from 2×106(cfu/mL) - 1×106(cfu/mL). The molds isolated were Aspergillus niger, Aspergillus flavus, Rhizopus microspores, Rhizopus arrhizus, Trichophyton mentagrophytes, Aspergillus fumigatus, Aspergillus nidulans and Trichophyton tonsurans. This study demonstrated that there are significant differences in the physicochemical properties and mycological characteristics of the various crops soil type analyzed. It also highlights that sustainable soil management boosts productivity.