Speaking as an electrician and not someone experienced with your particular lights.............
I'm assuming your system is dropping voltage to 48,24, or 12 volts. The standing water may not effect the low voltage lighting right away, but could cause problems down the road with corrosion. What is very important is to make sure the 120v side of the system is not exposed to the elements especially water. If you splice more wire into the system voltage is going to drop from the resistance of the extra wire. Adding some wire here and there probably will not hurt. But if you get carried away adding wire the voltage drop will be enough that the lights will not work.

You can buy wire nuts that have sealant inside of them.

I have sealed brushed nickel less-expensive Malibu lights in my yard. I live in Canada and get lots of snow. I do not bring my lights for the winter and in the spring they are usually quite wet and have water inside. I haven't had any problems thus far... I just let them dry out before running them on the transformer and they work just fine (for the last 5 years). They are made to be outside in the moisture... provided they are not installed in the bottom of a swamp!

In terms of splicing I would really try to avoid it if possible. Instead try looping the wire to and from the destination point rather than splice it in. But just ensure that your transformer is properly rated for both the total length of the wire and the total sum of the voltage of all lights along the run. The manufacturer will have details on this for you.

Feel free to ask any other questions... I just did a fairly large 25 light install with 900W (3x300) transformer for a friend. Was actually a nice job to do on a nice sunny day with friends + beer in hand. :)

I actually just installed a low voltage system yesterday. I installed a 600W Malibu Transformer, but I'm having an issue. I have two 12 gauge wire runs, one about 75 feet with six 20W cannon fixtures and all is well with this one. I also have one that is about 175 feet with three 50W well lights and then four 20W cannon lights. This line is where I have the issues. The four cannon lights are noticeably more dim than the ones on the other run. Any thoughts? I'm thinking it may be a voltage drop issue, but everything I read suggests that the transformer, gauge and distance should be fine.

Below is a chart I often refer to.

I prefer 10 gauge wire and connect all wires with waterproof caps. Wire caps

The quick connectors that come with most Malibu lights will not hold up over time and the connection is got as good. Just cut the quick connectors off and twist the wire together.

Here is a link that might be useful: low voltage wire

Thanks, looks like I will cut the wires and see how that works out. I guess I could drop the 50W bulbs down a little or tap these four issue lights into the other string, but then I need to figure out how to get across a walkway in a hidden manner...preferably not under. Been there, done that, not fun!