Marine sponges are hosts to dense and diverse microbial consortia that are likely to play a key role in the metabolic processes of the host sponge due to their enormous abundance. Common symbioses between nitrogen transforming microorganisms and sponges indicate complex nitrogen cycling within the host. Of particular interest is determining the community structure and function of microbial symbionts in order to gain deeper insight into host-symbiont interactions. We investigated the abundance and activity of microbial symbionts in two Mediterranean sponge species using quantitative real-time PCR. An absolute quantification of functional genes and transcripts in archaeal and bacterial symbionts was conducted to determine their involvement in nitrification and denitrification, comparing the low microbial abundance (LMA) sponge Dysidea avara with the high microbial abundance (HMA) representative Aplysina aerophoba. Absolute quantification of archaeal amoA-genes provided evidence of highly abundant ammonia-oxidizing archaea (AOA) in both HMA and LMA sponge species. Interestingly, detected amoA-transcripts indicated the activity of AOA only in the HMA representative. The variable abundance of AOA in chimneys within the A. aerophoba colony suggested an irregular distribution of symbionts. Moreover, denitrifying bacteria could be identified in A. aerophoba by using the functional gene marker, nirK. A high abundance of nitrite-reducing bacteria were detected based on cell numbers, and transcript counts revealed the bacterial activity. An experimental inhibition of pumping activity of A. aerophoba led to decreased activities of aerobic archaeal nitrifiers, whereas anaerobic denitrifying bacteria showed enhanced activity during non-pumping periods. This study revealed strong effects of pumping activity on nitrogen cycling in sponges, emphasizing the role of interactions between sponges and their symbionts.