Effective deconstruction of algal biomass is a major challenge associated with algal biofuels/bioproduct production. Improving biomass conversion requires understanding how reaction parameters affect the scale-up of bench scale processes to move to cost-effective conversion. Pretreatment of both aquatic and terrestrial feedstocks, using similar reaction conditions, identical feedstock and pretreatment chemistries have reported wide ranges in total sugar yields. This has been attributed to differences in reactor size or scale, type of operation (batch vs continuous), method of heating, reactor geometry and solids loading (w/w). These factors can impact both mass and heat transfer affecting both yield and reaction kinetics. To understand how total sugar yields in algal biomass are affected by different dilute acid pretreatment configurations we evaluated total sugar and lipid release at three reactor scales ranging from 4 ml to 300 ml, operated under mixed and non-mixed regimes.