How can I clean my Holy Water bottle? The Holy Water has sediment and the lid looks dirty
How can one clean my Holy Water bottle?
First of all, drain any remaining holy water directly into the ground, then wash normally.
Try filling the bottle with hot water and some form of soap. If need be use a brush to aid in the cleaning.
The contents should be then poured into the ground in a area where in would not be trampled on by human moment in the area.
Disposing of Sacramentals
When a material sacramental becomes so worn that it can no longer be used as a sacramental, one should not casually toss it into the trash. To prevent desecration, the sacramental should be returned to the earthly elements. Holy water, for example, should be poured into a hole dug in the earth, in a spot no one would walk over. Combustible sacramentals, such as scapulars and holy books, should be burned and then buried. Larger sacramentals that do not burn should be altered so that their form no longer appears to be a sacramental (for example, a statue should be broken up into small pieces) and then buried. Objects made of metals can be melted down and used for another purpose.
Items lose their blessing or consecration if they are desecrated, if they are substantially broken such that they can no longer be used for their sacred purpose, or if they are publicly sold. If an item is sold by one individual to another for only the price of the material itself, that is, if no profit is made, the blessing remains. For example, if you were to give someone a blessed rosary or sell it to him at cost, he would not have to have it re-blessed. If you were to sell a blessed rosary to someone for profit, he would need to take it to a priest to be blessed. - Sacramentals
Drain the holy water directly into the ground, then wash normally.
According to the Wikipedia page on holy water, the Catholic Church disposes of holy water by pouring it directly onto the ground (and they often have special disposal basins with plumbing directly connected to the ground called sacrariums that are used for this purpose); once the holy water has been disposed of, the container is then washed normally. It should be noted that holy water is not to be disposed of through normal plumbing.
That said, because of the ongoing Covid-19 pandemic, it's possible that Catholic Churches in your area should have already disposed of holy water in their fonts and stoups for fear of infection; you may want to talk to your priest to find out if any of these directive apply to your diocese.