Water pipe smoking is highly prevalent in developing countries, especially in Eastern Mediterranean regions. Research finds that more than 100 million people smoke a water pipe. Furthermore, tobacco smoking is one of the leading behavioral factors related to an increased risk of cancer, a leading cause of death globally. We aim to introduce a novel filtration system for water-pipe smoking and evaluate cytotoxic effects of common water pipe condensed smoke in comparison with our novel filtration system on normal (HEK293t) and cancer cell lines (Hep3B and MCF7) by MTS assay, alpha-fetoprotein (aFP), and apoptosis/necrosis effects. More so, the smoke substituents' neurotoxicity effect was evaluated by analyzing the depressive property on AMPA receptors (AMPARs). Our results showed that the silica filtration system was more effective than the water filtration system. The number of toxic compounds was reduced from 145 mg in distilled water extract (DWE) to 57.5 mg in silica solution extract (SSE). The SSE method also showed lower toxicity impacts on normal and cancerous cell lines (HEK293t, Hep3B, and MCF7) with CC50 values 149.9, 10.14, and 8.9 µg/ml, relative to the DWE method (CC50 values 77.1, 3.1, and 5.24 µg/ml, respectively). SSE extraction also reduced the α-FP (tumor marker test) to 2273.3 ng/ml which was closer in value to untreated cells (4066.7 ng/ml) in comparison with DWE which reduced it greatly to 1658.7 ng/ml, and the biophysical properties of AMPAR subunits demonstrate a reduced effect on desensitization rates of GluA2 homomer and GluA1/2 heteromer, using SSE relative to DWE. In conclusion, the condensed smoke of ordinary water pipe (DWE) has cytotoxic and neurotoxic impacts on various cell lines, while our newly developed system (SSE) was less toxic.