Your argument that they live in the wild and are exposed to the same rain is invalid. The wild is not an enclosure in your home. The rain does not directly fill a pond. The majority of the water volume gets in there after being filtered by plants and soil as runoff. Your intentions to NOT use "chemicals" is admirable, but ultimately misguided.
I have an ongoing experiment in rainwater collection and recycling. I will lay out the details and present you with my methods and preliminary results.
ABSTRACT
I started rainwater collection due to the high levels of atrazine, a herbicide that causes amphibians to "turn" into females. I live smack dab in the middle of the highest concentration use of atrazine in the world. You can see the issue with this throughout the forums in my posts as I have ended up with very skewed sexing of my home bred amphibians. That is, I get an extremely low percentage of males. Ultimately this wiped out my axolotl colony as I have 14 females and no males. Testing and experimentation shows this is directly correlated to the high levels of atrazine in our tap water. I felt this was necessary as water contaminants end up in significantly higher concentrations due to the nature of indoor enclosures.
SAMPLING AND INITIAL TESTING
Initially I collected 110 gallons of rainwater and snow melt over a six month period in two PETE drums lined with PTFE lab-liners. The water was analyzed through a series of tests both in the lab and with standard off the shelf kits for hobbyists. Here are the average results of 30 samples from this "hoard":
pH range 5.5-8.2 dependent on season and weather sample was taken
total hardness 110 ppm
carbonate hardness <100ppm
tested positive for lead, copper, and atrazine, sulfur compounds
atrazine levels @ 440 ppm
after treatment in a centrifugal, approximately 1.9 mL of unidentified solids were precipitated per 150mL samples
as a control, my tapwater tested out as:
pH range 5.5-8.2 dependent on season and weather sample was taken
total hardness 440 ppm
carbonate hardness 380-480ppm
tested positive for copper and atrazine
atrazine levels @ 320 ppm
after treatment in a centrifugal, approximately .3 mL of unidentified solids were precipitated per 150mL samples
After gas chromatography, the presence of higher than normal levels of various hydrocarbons, sulfur compounds and assorted heavy metals including lead, cobalt, and interestingly enough aluminum were present in all samples. Also the presence of chloramine and various bromides used in municipal water treatment were present.
These results make sense as I am downwind of a major airforce base and two freeways. Additionally there are foundries, slaughter houses, and chemical processing plants, in addition to thousands of acres of open farmland.
In short, the level of particulate concentration and contamination is very high.remember rain and snow forms thanks to particulate matter in the air. Without it, the water vapor has no surface to condense on.
In your case, you location in the Flagstaff area means you also get a triple threat of airborne contaminants thanks to Mexico, Southern California, and the irrigation practices in your state. Winds also carry a significant amount of desert dust which I am certain adds a whole range of contaminants I do not get here.
PREPARATION OF COLLECTED RAINWATER FOR AQUARIUM USE
After significant research, I devised a five stage filtration, purification and treatment of this water.While the easiest method would be to RO/DI the water, then age it with limestone and samples from established pond tanks, I took a different approach to see just what it takes to "make" water suitable for amphibians without spending thousands.
First the water was pumped through a 55 gallon drum (like the holding tanks described earlier) through three stages. Stage one was a layer of greensand. Stage two was a layer of limestone gravel and stage three was a layer of activated carbon.
Testing of this initial stage provided similar results, although the desired effect of increased hardness and stabilized pH were successful. Other results were the same, or comparable to expected results due to the action of the greensand and the carbon. I should note here that atrazine levels were unaffected. The next stage was to treat the water with an off the shelf aqueous solution of sodium thiosulfate (Amquel+ and NovAqua) to ease the removal of various metals. Testing here showed the expected results, so the next stage the water was recirculated through the first drum. Then, pumped into a holding drum, the water was exposed to UV sterilization for 24 hours. The desired effect here was achieved as atrazine breaks down in UV. This worked extremely well, as atrazine was no longer detectable but the products lowered the pH to 4.8. This water was then treated and aged with a ratio of 1Kg of crushed limestone and one ounce of modified Holtfretter's Solution per five gallons of water. Additionally the water was cooled to 15C and aerated with ozone and oxygen. After a final stage of settling and activated carbon filtration, the water was allowed to age for 30 days after the addition of a "live" culture sample from a long established indoor, amphibian free pond tank.
The results are as follows:
pH range 6.8-7.2 dependent on season and weather sample was taken
total hardness 440 ppm
carbonate hardness 400ppm
tested negative for lead, copper, and atrazine, sulfur compounds
atrazine levels none detected
after treatment in a centrifuge, approximately 2.3 mL of solids were precipitated per 150mL samples (all solids Identified as biological detritus as would be expected from the ageing stage)
RESULTS thus far
After this lengthy process, I determined that collecting rainwater and using it unprocessed is just as detrimental to amphibians as untreated tap water. I now utilize my rainwater collection for gardening instead. It is more cost and time effective to treat tapwater in the normal hobbyist proscribed manner and then expose it to intense UV to destroy the atrazine. I utilize additional aging and filtration to achieve what I consider to be optimal chemistry for the species I keep.
In other words, don't assume the precipitation is "safe". Thanks to humanity, it is just as polluted and laced with chemicals as everything else.
