Abstract. Chloropigment and particulate organic carbon (POC) concentration data collected using in-situ large-volume pumps during the MedFlux project in the Mediterranean Sea in May 2005 provided an opportunity to estimate rate constants that control the fate of particles and specifically chloropigments in the water column. Additionally, comparisons to thorium and chloropigment data from settling-velocity (SV) sediment traps at the same site enabled us to distinguish between the influence of the sampling method used vs. the tracer used on particle dynamic rate constants. Here we introduce a Bayesian statistical inversion method that combines the data with a new box model and has the capacity to infer rate constants for POC respiration/dissolution, chlorophyll and phaeopigment degradation, and particle aggregation and disaggregation. The estimated small-particle (1–70 μm) POC respiration rate constant was 1.25+0.55−0.38 yr⁻¹ (0.80 yr). For this data set, the rate constants for chlorophyll (Chl) degradation to phaeopigments and phaeopigment respiration were not well constrained. The estimated aggregation and disaggregation rate constants were 7.65+3.35−2.33 (0.13 yr) and 106.09+39.13−28.59 yr⁻¹ (0.01 yr), respectively, which indicates that particle aggregation and disaggregation were extensive at the studied depths (125–750 m) in May after the spring bloom had ended and flux was low.