Patients on peritoneal dialysis (PD) encounter peritoneal functional and structural alterations. It is still unknown whether levels of plasminogen activator inhibitor type 1 (PAI-1), matrix metalloproteinases- (MMP-) 2, and vascular endothelial growth factor (VEGF) exhibit dynamic changes in peritoneal effluents. The aim of the present study was to investigate the longitudinal changes in these biomarkers in PD patients and their association with peritoneal small-solute transfer rate (PSTR). This prospective, single-center cohort study included 70 new PD patients. The presence of PAI-1, MMP-2, and VEGF in peritoneal effluents was measured regularly after PD initiation. The association between those biomarkers and 4-hour effluent:plasma creatinine ratio (PSTR) was analyzed. Longitudinal follow-up showed a tendency for PAI-1 (p < 0.001) and VEGF (p = 0.04) to increase with the duration of PD. Both PSTR at baseline and PSTR at 2 years significantly associated with PAI-1, MMP-2, and VEGF levels at baseline. PSTR at 2 years also associated with the MMP-2 level at 6 months and PAI-1 level at baseline. The present study illustrated a positive association of PSTR with selected biomarkers in peritoneal effluents observed over a 2-year period.