So my wife poo-pooed the SteriPen... Are lakes more problem?

There are not really viruses in the water sources. Bacteria and Protozoa, yes. Giardia and Crypto have a long incubation period... people who get sick on the trail generally have some lesser infection going on, perhaps tummy troubles related to a big change in diet, which happens when you go buy a bunch of cruddy freeze dried meals.... If there is not really horrible diarrhea and really bad gas and terrible stomach cramps, it's not a bad giardia infection. Altho, different people do react differently - a lab test would have to happen to confirm.

Lakes and streams are all the same water as each other -- streams come out of lakes, after all. There has been a theory that the top layers of water on a lake can be sterilized by the UV of the sun. However, no one's come up with a study to prove that... filtering, sterilizing with chemicals, or boiling still very much recommended especially along the JMT where pack animals and hundreds of people are stepping in, swimming in, sitting in, possibly sh***ing in, the water. No matter whether it is still or running.

Yeah, both your theories sound more reasonable. I guess I was thinking viruses because of the extreme situation in Rio (super bacteria AND viruses). I think my wife & daughter are cooking exclusively from freeze dried meals (all purchased at REI). However, my daughter is a vegetarian, an I think my wife decided to go along with the 100% vegetarian pouch cooking -- might have been a shock to her system

Nevertheless, on our two previous JMT segment hikes, we filtered and then used the SteriPen, which I have previously agreed might have been overkill -- but we never had any food / water born illness.

I also cautioned them not to let an unfiltered water source contact a clean/filtered/sterilized container of water. But that's less likely with the way the Sawyer gravity system works (brilliantly, I think -- and very, very fast).

Not sure where I read that it was always better to pull from a running stream -- I think that running water is more likely to get oxygenated, and running water is more likely to dilute any local concentration of bacteria that might collect in a still pool.

I was thinking about Dissolved Oxygen (DO).

water.usgs.gov/edu/dissolvedoxygen.html

And while DO directly relates to the health of a body of water, it does not, in itself, lead to removing bacteria -- especially oxygen-loving bacteria -- from the water.

I'm fairly certain the .1 micron filter on the Sawyer is good for the bacteria, protozoa, giardia, salmonella and cryptosporidia. I knew the SteriPen disrupted the genetic material.

If I had done my homework (or had listened to High Sierra Fan), I would've read this great article by Robert W. Derlet:

"Furthermore, no documented cases of viral acquired illnesses can be traced from drinking water from Sierra streams or lakes. Purification to kill viruses in most backcountry acres of the Sierra is not necessary."

So is there absolutely no difference in pulling from a stream vs a lake?

You may have hit the nail on the head, along with altitude.