Biofilms are spatially organized microorganism colonies embedded in a self-produced matrix, conferring to the microbial community resistance to environmental stresses. Motile bacteria have been observed swimming in the matrix of pathogenic exogeneous host biofilms. This observation opened new promising routes for deleterious biofilms biocontrol: these bacterial swimmers enhance biofilm vascularization for chemical treatment or could deliver biocontrol agent by microbial hitchhiking or local synthesis. %\cite{muok2021microbial,yu2020hitchhiking,samad2017swimming}. Hence, characterizing swimmer trajectories in the biofilm matrix is of particular interest to understand and optimize its biocontrol. In this study, a new methodology is developed to analyze time-lapse confocal laser scanning images to describe and compare the swimming trajectories of bacterial swimmers populations and their adaptations to the biofilm structure. The method is based on the inference of a kinetic model of swimmer population including mechanistic interactions with the host biofilm. After validation on synthetic data, the methodology is implemented on images of three different motile {Bacillus species swimming in a Staphylococcus aureus biofilm. The fitted model allows to stratify the swimmer populations by their swimming behavior and provides insights into the mechanisms deployed by the micro-swimmers to adapt their swimming traits to the biofilm matrix.