The quantification and comparison of microplastic contamination of sediments are affected by sample heterogeneity and the systematic and random effects affecting sample analysis. The quantification and combination of these components in the measurement uncertainty allows the objective interpretation of analysis results. This work presents the first detailed evaluation of the uncertainty of microplastic contamination quantification in sediments. The random and systematic effects affecting microplastic counts are modeled by the Poisson-lognormal distribution with inputs estimated from duplicate sediment analysis and the analysis of sediments spiked with microparticles. The uncertainty from particle counting was combined with the uncertainty from the determination of the dry mass of the analytical portion by the Monte Carlo method. The developed methodology was implemented in a user-friendly spreadsheet made available as the Supporting Information. The contamination of sediment samples collected in various inland Portuguese waters was determined, ranging from [0; 160] to [361; 2932] kg–1 for a 99% confidence level, and compared by assessing if the difference between contamination levels is equivalent to zero for the same confidence level. Several samples proved to have metrologically different microplastic contamination. This work represents a contribution to the objectivity of the assessment of environmental contamination with microplastics.