Quantification of biogeochemical rates is essential to the understanding of the dynamics of aquatic ecosystems. However, this has proven to be difficult to achieve especially under conditions of high spatial and temporal hydrodynamic and biogeochemical variability. Here, a Lagrangian experimental design was employed to estimate biogeochemical rate coefficients in situ. A set of four drogues and a cross-transect sampling design was used to capture the patchy distribution of phytoplankton and nutrient species, and high transport and mixing rates. A mass balance approach was applied to a Lagrangian control volume moving with a drogue. This approach was used to separate internal biogeochemical changes from the physical changes due to advection, diffusion, and convergence/divergence fluxes. This experimental approach was applied to an oligotrophic coastal region. The phytoplankton growth rate, primary production, and carbon to chlorophyll ratio (C: Chla) obtained from the experiment agreed with the highest literature values for this study site. This supported the validity of this approach. The effect of scales of processes and patchiness is highlighted from this experiment. It is shown that the experimental design is subject to a relationship between size of the control volume, the time scale of internal processes, and sampling time.