I am still interested in visiting - Pto. Vallarta has some nice aspects to it.

However, some of the area beaches ARE contaminated - the closer you get to the mouth of the Cuale River, the more polluted it is. In July of 2012, the measurement of enterococci per 100 ml was 3,076 (and Mismaloya came in at 728); the latter in particular reflects truly horrendous numbers. OTOH, Boca de Tomatlán and Playa de los Muertos were within sanitary norms.

In nearby Nayarit, Sayulita was at unhealthy levels, whilst La Crúz de Huanacaxtle and Bucerías were within acceptable limits. These numbers have been reported to COFEPRIS (Comisión Federal para la Protección contra Riesgos Sanitarios) by the health departments of Nayarit and Jalisco states.

During the rains, which normally are occurring ~May or June - October, the pollution can be quite severe - and include everything from pesticides and fertilizers to human fecal bacteria. I have been visiting the area since the 1970s, and am quite familiar with the issues and some of the problems (construction that has been allowed with insufficient sewage handling, for example), and I can read the newspapers and websites that detail the issue better and more transparently than, say, the Mexican tourism bureau (SECTUR, the Secretaría de Turismo), which is quite hesitant to admit anything that would inhibit visitors to Mexico. Though the states of Jalisco and Nayarit and the Federal authorities have been working on this issue, it is not fully fixed yet.

A number of Mexican beach areas are severely contaminated - Acapulco probably leads the bunch - and it would be insanely naive to ignore these facts and not take precautions. I have gone for years (including Acapulco and Zihuatanejo, since the early 1950s) and still go - but I do take some precautions and avoid the worst problem areas as reported.