Biofouling and microbiologically influenced corrosion are major concerns to the long-term integrity of nuclear waste storage basins. The results of long-term microbial monitoring of nuclear storage at the Savannah River Site L-Basin nuclear material storage facility were examined to determine corrosion potential and biofouling. The densities of specific microbial species that can impact microbial corrosion and biofouling, including sulfate-reducing bacteria (SRB) and acid-producing (e.g., iron-oxidizing) bacteria (APB), were quantified by colony forming units (CFU). Several trends in microbial activity were observed during this time period. Overall microbial densities decreased slightly between 2000 and 2012. Metabolic diversity of microorganisms as measured by BIOLOG™ also decreased dramatically during this time. Aerobic microbial densities decreased from 2001 to 2010. Aerobes were most prevalent at 3.23 average CFU/mL and APB densities were lower at 0.80 average CFU/mL. From 2017 to present, iron-reducing bacteria were most prevalent at 3.41 average CFU/mL and APB were least prevalent at 0.44 average CFU/mL. All bacterial densities decreased except that of low-nutrient bacteria, which averaged 2.90 CFU/mL, and SRB averaged 0.19 CFU/mL. No distinct correlations between microbial concentrations, temperature, and either water chemistry parameters (pH and conductivity) or radiological conditions (19–30 disintegrations per minute (DPM) beta-gamma/mL; the equivalent to 0.32–0.50 Bq per mL) were determined. The occurrence of microbial biofilm formation on storage cannisters created biofouling issues in recent years. Although cleaning the biofouled surfaces provided temporary relief, the biofouling returned. Based on these results and physical observations of coupons, there has been minimal evidence of corrosion to date.