This study investigated the relationship between variations in pH and electrical conductivity (EC) with the degradation of total organic carbon (TOC) and total nitrogen (TN) in agro-industrial effluents, specifically apple boiling water and digestate derived from apple boiling water subjected to dark fermentation. Substrates partly composed of agricultural waste, such as ground corn cobs and hazelnut shells, were used. These substrates were tested in two 28-day batch tests and three column tests, two lasting 6 hours and one 12 days, in contact with the agro-industrial effluents to determine the optimal substrate for their degradation. The results showed that corn cobs were unsuitable for this purpose, whereas hazelnut shells achieved over 90% TOC degradation from the digestate and more than 40% from the apple boiling water.