The long-term performance of chronic microelectrode array implants for neural ensemble recording is affected by temporal degradation in signal quality due to several factors including structural changes in the recording surface, electrical responses, and tissue immune reactivity. This study combines the information available from the temporal aggregation of both biotic and abiotic metrics to analyze and quantify the combined effects on long-term performance. Study of a 42-day implant showed there was a functional relationship between the measured impedance and the array neuronal yield. This was correlated with structural changes in the recording sites, microglial activation/degeneration, and elevation of a blood biochemical marker for axonal injury. We seek to elucidate the mechanisms of chronic microelectrode array failure through the study of the combined effects of these biotic and abiotic factors.