The example you give isn't directly runable, (see reprex) so I can't say for certain if this works.
Date conversion
Try something like the following to convert the "Date" column to a Date class.
library(lubridate)
TomDO<- ts(Tom_Frost_Dissolved_Oxygen)
# Convert to Date class
TomDO$Date <- mdy(TomDO$Date)
autoplot(TomDO, ts.geom = 'ribbon', fill = 'blue')
Pivot the data longer
Maybe autoplot is getting messed up by the catgorical nature of the columns. Let's convert the data to a longer format. To do this it used to be melt or gather, but now it's pivot_longer.
library(tidyr)
library(tibble)
library(dplyr)
TomDO <- tribble(~Top, ~Middle, ~Bottom, ~Date,
12.55, 13.39, 9.55, "3/9/15",
6.8, 6.55, 0.36, "3/31/15",
7.22, 6.64, 6.01, "4/13/15",
7.22, 6.64, 6.01, "4/13/15")
# Date class conversion
TomDO$Date <- mdy(TomDO$Date)
# Make long format data
pivoted_df <- pivot_longer(TomDO, cols=c("Top", "Middle", "Bottom"), names_to="Layer")
# plot!
autoplot(pivoted_df, ts.geom="ribbon")
# Error: Objects of type tbl_df/tbl/data.frame not supported by autoplot.
Huh... what kind of object is TomDO?
autoplot(ts(pivoted_df), ts.geom="ribbon")
# Error: Objects of type mts/ts/matrix not supported by autoplot.
Reproducible example needed.
Well.... we tried some thing and found some errors. Can you provide a reproducible example?