Within the anaerobic and aerobic environment, various important parameters affect the rates of the different steps of the process, i. e. pH and alkalinity, temperature, and hydraulic retention times.

Each group of microorganisms has a different optimum pH range. Methanogenic bacteria are extremely sensitive to pH with an optimum between 6.5 and 7.2 pH, alkalinity and volatile acids/alkalinity ratio. The fermentative microorganisms are somewhat less sensitive and can function in a wider range of pH between 4.0 and 8.5. at a low pH the main products are acetic and butyric acid, while at a pH of 8.0 mainly acetic and propionic acid are produced.

The temperature has an important effect on the physicochemical properties of the components found in the digestion substrate. It also influences the growth rate and metabolism of microorganisms and hence the population dynamics in the anaerobic reactor. Acetotrophic methanogens are one of the most sensitive groups to increasing temperatures. The degradation of propionate and butyrate is also sensitive to temperatures above 70 °C. The temperature has moreover a significant effect on the partial pressure of H2 in digesters, hence influencing the kinetics of the syntrophic metabolism. Thermodynamics show that endergonic reactions (under standard conditions), for instance the breakdown of propionate into acetate, CO2, H2, would become energetically more favourable at higher temperature, while reactions which are exergonic (e. g. hydrogenotrophic methanogenesis) are less favoured at higher temperatures.

The solids retention time (SRT) is the average time the solids spend in the digester, whereas the hydraulic retention time (HRT) is the average time the liquid sludge is held in the digester. The subsequent steps of the digestion process are directly related to the SRT. A decrease in the SRT decreases the extent of the reactions and viceversa. Each time sludge is withdrawn, a fraction of the bacterial population is removed thus implying that the cell growth must at least compensate the cell removal to ensure steady state and avoid process failure [28].